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GitLab

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<h3>

Andreas Tille pushed to branch master

at <a href="https://salsa.debian.org/med-team/mapsembler2">Debian Med / mapsembler2</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/mapsembler2/commit/4d7c7bb99025b58bb8be150e794bd1d45062c608">4d7c7bb9</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-10-10T08:46:33Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debhelper 11

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/mapsembler2/commit/d3e34cafabbdf3aeaf65a498520eed144e8a59c6">d3e34caf</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-10-10T08:46:36Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Point Vcs fields to salsa.debian.org

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/mapsembler2/commit/c4d3cafee095734b611fb336927f00ca3c594015">c4d3cafe</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-10-10T08:46:37Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.2.1

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/mapsembler2/commit/336f9bd5deda157e34b743023d131d5d23a6a3ea">336f9bd5</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-10-10T09:48:21Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Drop unneeded get-orig-source target

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/mapsembler2/commit/f41824136ce0b5dfe4b03b98d241ee2634eef08a">f4182413</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-10-10T10:04:43Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Drop unused patches

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/mapsembler2/commit/c4f27d3e707453702eef8f8f2b004fdacbdb1b4e">c4f27d3e</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-10-10T10:06:49Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Do not parse d/changelog

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/mapsembler2/commit/05b2aa22d4c353900d06f2b124e6920241a4c333">05b2aa22</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-10-10T10:50:19Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix spelling

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/mapsembler2/commit/8be74535d7e680fa0e91eaad3f0f6516ad8a5a9b">8be74535</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-10-10T11:06:08Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Create manpages before package creation

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/mapsembler2/commit/366d3c1bdedd5be42f9fcdc3a44792f445a23695">366d3c1b</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-10-10T11:21:11Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Manual edits of manpages

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/mapsembler2/commit/5154ff6485069ccb90c2c8c6bf622e54b7bc86a5">5154ff64</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-10-10T11:42:31Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Re-add renaming of tools

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/mapsembler2/commit/c9b0cf430f84857eb2cdd36ec3b1e6820f9e4d9f">c9b0cf43</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-10-10T13:00:37Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix manpage installation

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/mapsembler2/commit/3f6a046f42cfd67ed124b31341454defacd9d138">3f6a046f</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-10-10T13:12:32Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable

</pre>

</li>

</ul>

<h4>16 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

</a>

</li>

<li class="file-stats">

<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">

debian/compat

</a>

</li>

<li class="file-stats">

<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

debian/control

</a>

</li>

<li class="file-stats">

<a href="#ebcf9854ee19af4b7bf8405b283789c18769680f">

<span class="new-file">

+

debian/createmanpages

</span>

</a>

</li>

<li class="file-stats">

<a href="#2fdff9655a32f6ef4adc51438d0993cb7bb38ecb">

<span class="new-file">

+

debian/mans/mapsembler2_extremities.1

</span>

</a>

</li>

<li class="file-stats">

<a href="#5d1be87f17e070a1304e79e50d9a4e89a1a6f07f">

<span class="new-file">

+

debian/mans/mapsembler2_kissreads.1

</span>

</a>

</li>

<li class="file-stats">

<a href="#6935db46e89a5d49d7a15ca8202a1f2fae9c3ffd">

<span class="new-file">

+

debian/mans/mapsembler2_kissreads_graph.1

</span>

</a>

</li>

<li class="file-stats">

<a href="#997e9ed24cbaf48602d1a5783f534367b993f182">

<span class="new-file">

+

debian/mans/mapsembler_extend.1

</span>

</a>

</li>

<li class="file-stats">

<a href="#105896cab3a29d651da9f1df968e932631fd91ee">

<span class="new-file">

+

debian/mans/run_mapsembler2_pipeline.1

</span>

</a>

</li>

<li class="file-stats">

<a href="#2599798e0a9deb7e9830d61d9024c3d8c0aee3be">

debian/mapsembler2.manpages

</a>

</li>

<li class="file-stats">

<a href="#4bf5c375f6de83c6b39cea4b73262a3f9f1e0002">

<span class="deleted-file">

−

debian/patches/fix_build

</span>

</a>

</li>

<li class="file-stats">

<a href="#b82cc53a96d198b42d2cf5ccdce4b085dbfb94ca">

<span class="deleted-file">

−

debian/patches/fix_makefile

</span>

</a>

</li>

<li class="file-stats">

<a href="#94fea411c7d9c972414b101a25bd83389ecffb01">

<span class="deleted-file">

−

debian/patches/fix_path

</span>

</a>

</li>

<li class="file-stats">

<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

debian/patches/series

</a>

</li>

<li class="file-stats">

<a href="#45ae034d1d71b2d961abb7c91cf3d2f1a02a59c6">

<span class="new-file">

+

debian/patches/spelling.patch

</span>

</a>

</li>

<li class="file-stats">

<a href="#8756c63497c8dc39f7773438edf53b220c773f67">

debian/rules

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/mapsembler2/compare/dd6a079ef642cf7cd2a0c4c9f215794aa6553401...3f6a046f42cfd67ed124b31341454defacd9d138#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1

</td>

<td class="diff-line-num new_line old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">mapsembler2 (2.2.4+dfsg-2) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">mapsembler2 (2.2.4+dfsg-2) <span class="idiff left right">unstable</span>; urgency=medium</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

</td>

<td class="diff-line-num new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">  [ Steffen Moeller ]</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

</td>

<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">  * Created debian/upstream/metadata</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

</td>

<td class="diff-line-num new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

5

</td>

<td class="diff-line-num new_line old" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> -- Steffen Moeller <moeller@debian.org>  Tue, 26 Sep 2017 14:38:54 +0200</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">  [ Andreas Tille ]</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">  * debhelper 11</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

8

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">  * Point Vcs fields to salsa.debian.org</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

9

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">  * Standards-Version: 4.2.1</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

10

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">  * d/rules:</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

11

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">     - Drop unneeded get-orig-source target</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">     - Do not parse d/changelog</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

13

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">  * Fix spelling</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

14

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">  * Create manpages before package creation</span>

</pre>

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15

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org>  Wed, 10 Oct 2018 15:07:09 +0200</span>

</pre>

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6

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"></span>

</pre>

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18

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">mapsembler2 (2.2.4+dfsg-1) unstable; urgency=medium</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

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<td class="diff-line-num new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

19

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>

</pre>

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<br>

</li>

<li id="78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">

<a href="https://salsa.debian.org/med-team/mapsembler2/compare/dd6a079ef642cf7cd2a0c4c9f215794aa6553401...3f6a046f42cfd67ed124b31341454defacd9d138#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong></a>

<hr>

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1

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<td class="diff-line-num new_line old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">1<span class="idiff left right">0</span></span></pre>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">1<span class="idiff left right">1</span></span></pre>

</td>

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</table>

<br>

</li>

<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

<a href="https://salsa.debian.org/med-team/mapsembler2/compare/dd6a079ef642cf7cd2a0c4c9f215794aa6553401...3f6a046f42cfd67ed124b31341454defacd9d138#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,17 +4,16 @@ Uploaders: Olivier Sallou <osallou@debian.org>,</td>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">           Andreas Tille <tille@debian.org></span>

</pre>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Section: science</span>

</pre>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Priority: optional</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper (>= 1<span class="idiff left right">0</span>),</span>

</pre>

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7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper (>= 1<span class="idiff left right">1~</span>),</span>

</pre>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">               cmake,</span>

</pre>

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9

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">               bc,</span>

</pre>

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10

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<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

</td>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">               zlib1g-dev,</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

11

</td>

<td class="diff-line-num new_line old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">               help2man,</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12

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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

11

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">               libhdf5-dev,</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13

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<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">               libcppunit-dev,</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14

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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">               libboost-dev</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

15

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<td class="diff-line-num new_line old" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">1.0</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

16

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<td class="diff-line-num new_line old" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">Vcs-Browser: https://<span class="idiff left right">anonscm.debian.org/cgit/debian-med/mapsembler2.git</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

17

</td>

<td class="diff-line-num new_line old" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">Vcs-Git: https://<span class="idiff left right">anonscm.debian.org/git/debian-med</span>/mapsembler2.git</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

14

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">2.1</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

15

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Vcs-Browser: https://<span class="idiff left right">salsa.debian.org/med-team/mapsembler2</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

16

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">Vcs-Git: https://<span class="idiff left right">salsa.debian.org/med-team</span>/mapsembler2.git</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

18

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<td class="diff-line-num new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

17

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Homepage: http://colibread.inria.fr/mapsembler2/</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

19

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<td class="diff-line-num new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

18

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

20

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<td class="diff-line-num new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

19

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Package: mapsembler2</span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="ebcf9854ee19af4b7bf8405b283789c18769680f">

<a href="https://salsa.debian.org/med-team/mapsembler2/compare/dd6a079ef642cf7cd2a0c4c9f215794aa6553401...3f6a046f42cfd67ed124b31341454defacd9d138#ebcf9854ee19af4b7bf8405b283789c18769680f"><strong>debian/createmanpages</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/sh</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nv" style="color: teal;">MANDIR</span><span class="o" style="font-weight: 600;">=</span>debian/mans</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: navy;">-p</span> <span class="nv" style="color: teal;">$MANDIR</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="nv" style="color: teal;">VERSION</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span>dpkg-parsechangelog | <span class="nb" style="color: #0086b3;">awk</span> <span class="s1" style="color: #d14;">'/^Version:/ {print $2}'</span> | <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'s/^[0-9]*://'</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'s/-.*//'</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'s/[+~]dfsg$//'</span><span class="sb" style="color: #d14;">`</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="nv" style="color: teal;">NAME</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">grep</span> <span class="s2" style="color: #d14;">"^Description:"</span> debian/control | <span class="nb" style="color: #0086b3;">sed</span> <span class="s1" style="color: #d14;">'s/^Description: *//'</span> | <span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: navy;">-n1</span><span class="sb" style="color: #d14;">`</span></span>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="nv" style="color: teal;">PROGNAME</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">grep</span> <span class="s2" style="color: #d14;">"^Package:"</span> debian/control | <span class="nb" style="color: #0086b3;">sed</span> <span class="s1" style="color: #d14;">'s/^Package: *//'</span><span class="sb" style="color: #d14;">`</span></span>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="nv" style="color: teal;">AUTHOR</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">".SH AUTHOR</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">This manpage was written by </span><span class="nv" style="color: teal;">$DEBFULLNAME</span><span class="s2" style="color: #d14;"> for the Debian distribution and</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="s2" style="color: #d14;">can be used for any other usage of the program.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="s2" style="color: #d14;">"</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="nv" style="color: teal;">progname</span><span class="o" style="font-weight: 600;">=</span>mapsembler2_extremities</span>

</pre>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell">help2man <span class="nt" style="color: navy;">--no-info</span> <span class="nt" style="color: navy;">--no-discard-stderr</span> <span class="nt" style="color: navy;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" "</span> <span class="se" style="color: #d14;">\</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell">         <span class="nt" style="color: navy;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"performs the first step of Mapsembler2_extend"</span> <span class="se" style="color: #d14;">\</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell">            <span class="nt" style="color: navy;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: teal;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: teal;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="nv" style="color: teal;">progname</span><span class="o" style="font-weight: 600;">=</span>mapsembler_extend</span>

</pre>

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell">help2man <span class="nt" style="color: navy;">--no-info</span> <span class="nt" style="color: navy;">--no-discard-stderr</span> <span class="nt" style="color: navy;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" "</span> <span class="se" style="color: #d14;">\</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell">         <span class="nt" style="color: navy;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"extends a DNA sequence of interest given a set of reads, by computing a targeted micro assembly"</span> <span class="se" style="color: #d14;">\</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell">            <span class="nt" style="color: navy;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

23

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: teal;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: teal;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"><span class="nv" style="color: teal;">progname</span><span class="o" style="font-weight: 600;">=</span>mapsembler2_kissreads</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

26

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell">help2man <span class="nt" style="color: navy;">--no-info</span> <span class="nt" style="color: navy;">--no-discard-stderr</span> <span class="nt" style="color: navy;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" "</span> <span class="se" style="color: #d14;">\</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell">         <span class="nt" style="color: navy;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"Checks for each sequence contained into the toCheck.fasta if it is read coherent with reads from readsA.fasta or readsB.fasta"</span> <span class="se" style="color: #d14;">\</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

28

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell">            <span class="nt" style="color: navy;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

29

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: teal;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: teal;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

30

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

31

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"><span class="nv" style="color: teal;">progname</span><span class="o" style="font-weight: 600;">=</span>mapsembler2_kissreads_graph</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

32

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell">help2man <span class="nt" style="color: navy;">--no-info</span> <span class="nt" style="color: navy;">--no-discard-stderr</span> <span class="nt" style="color: navy;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" "</span> <span class="se" style="color: #d14;">\</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

33

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell">         <span class="nt" style="color: navy;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"maps the provided reads on the graph"</span> <span class="se" style="color: #d14;">\</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell">            <span class="nt" style="color: navy;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

35

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: teal;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: teal;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

36

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell"><span class="nv" style="color: teal;">progname</span><span class="o" style="font-weight: 600;">=</span>run_mapsembler2_pipeline</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

38

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell">help2man <span class="nt" style="color: navy;">--no-info</span> <span class="nt" style="color: navy;">--no-discard-stderr</span> <span class="nt" style="color: navy;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" "</span> <span class="se" style="color: #d14;">\</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell">         <span class="nt" style="color: navy;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"pipelines the mapsembler2 tools"</span> <span class="se" style="color: #d14;">\</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="shell">            <span class="nt" style="color: navy;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: teal;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: teal;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>

</pre>

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="shell"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$MANDIR</span><span class="s2" style="color: #d14;">/*.1"</span> <span class="o" style="font-weight: 600;">></span> debian/manpages</span>

</pre>

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="shell"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: teal;">EOT</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="shell"><span class="sh" style="color: #d14;">Please enhance the help2man output.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="shell"><span class="sh" style="color: #d14;">The following web page might be helpful in doing so:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="shell"><span class="sh" style="color: #d14;">    http://liw.fi/manpages/</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="shell"><span class="no" style="color: teal;">EOT</span></span></pre>

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<br>

</li>

<li id="2fdff9655a32f6ef4adc51438d0993cb7bb38ecb">

<a href="https://salsa.debian.org/med-team/mapsembler2/compare/dd6a079ef642cf7cd2a0c4c9f215794aa6553401...3f6a046f42cfd67ed124b31341454defacd9d138#2fdff9655a32f6ef4adc51438d0993cb7bb38ecb"><strong>debian/mans/mapsembler2_extremities.1</strong></a>

<hr>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.7.</span>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH MAPSEMBLER2_EXTREMITIES "1" "October 2018" "mapsembler2_extremities 2.2.4" "User Commands"</span>

</pre>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.SH NAME</span>

</pre>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">mapsembler2_extremities \- performs the first step of Mapsembler2_extend</span>

</pre>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>

</pre>

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6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.B mapsembler2_extremities</span>

</pre>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">\fB\-\-k\fR <kmersize> \fB\-\-starters\fR <fasta> \fB\-\-reads\fR <dataset> \fB\-\-output\fR <substarterfile> [optional arguments]</span>

</pre>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.SH DESCRIPTION</span>

</pre>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">This modules performs the first step of Mapsembler2_extend. For each starter, it outputs a list of extremities of the starter (of length *k*) are found in the reads, up to 1 indel or mismatch.</span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

10

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">.SH OPTIONS</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

11

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">.TP</span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">\fB\-\-k\fR (1 arg):</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

13

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">kmer size that will be used for mapsembler2  [default '']</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

14

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">.TP</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

15

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">\fB\-\-starters\fR (1 arg):</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

16

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">starters fasta file  [default '']</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

17

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">.TP</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

18

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">\fB\-\-reads\fR(1 arg):</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

19

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">reads dataset file name. Several reads sets can be provided, surrounded by "'s and separated by a space (e.g. \fB\-\-reads\fR "reads1.fa reads2.fa")  [default '']</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

20

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">.TP</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

21

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">\fB\-\-output\fR (1 arg):</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

22

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">output substarters file name  [default '']</span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

23

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">.TP</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

24

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">\fB\-\-min\-solid\-subkmer\fR (1 arg):</span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

25

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">minimim abundance to keep a subkmer  [default '3']</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

26

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">.TP</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

27

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">\fB\-debug\fR (0 arg):</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

28

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">debugging</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

29

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">.TP</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

30

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">\fB\-nb\-cores\fR (1 arg):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">number of cores  [default '0']</span>

</pre>

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">.TP</span>

</pre>

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">\fB\-verbose\fR (1 arg):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">verbosity level  [default '1']</span>

</pre>

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">.TP</span>

</pre>

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">\fB\-help\fR (0 arg):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">display help about possible options</span>

</pre>

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">.SH AUTHOR</span>

</pre>

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.</span></pre>

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<br>

</li>

<li id="5d1be87f17e070a1304e79e50d9a4e89a1a6f07f">

<a href="https://salsa.debian.org/med-team/mapsembler2/compare/dd6a079ef642cf7cd2a0c4c9f215794aa6553401...3f6a046f42cfd67ed124b31341454defacd9d138#5d1be87f17e070a1304e79e50d9a4e89a1a6f07f"><strong>debian/mans/mapsembler2_kissreads.1</strong></a>

<hr>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.7.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH MAPSEMBLER2_KISSREADS "1" "October 2018" "mapsembler2_kissreads 2.2.4" "User Commands"</span>

</pre>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.SH NAME</span>

</pre>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">mapsembler2_kissreads \- Checks for each sequence contained into the toCheck.fasta if it is read coherent with reads from readsA.fasta or readsB.fasta</span>

</pre>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>

</pre>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.B mapsembler2_kissreads</span>

</pre>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"><toCheck.fasta> <readsC1.fasta> [<readsC2.fasta> [<readsC3.fasta] ...] [\-k value] [\-c value] [\-d value] [\-O value] [\-o name] [\-u name] [\-n] [\-I] [\-i index_stride] [\-m align_file] [\-s] [\-f] [\-h]</span>

</pre>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.SH DESCRIPTION</span>

</pre>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Checks for each sequence contained into the toCheck.fasta if</span>

</pre>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">it is read coherent (each position is covered by at least "min_coverage" read(s)) with reads from readsA.fasta or readsB.fasta</span>

</pre>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">A sequence s from toCheck is treated as follow:</span>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">.IP</span>

</pre>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">if (s coherent with at least one read set): output the sequence as follows</span>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">.IP</span>

</pre>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">>original fasta comment|C1:min<avg\-corr_avg<max|C2:min<avg\-cor_avg<max|C3...:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">>s</span>

</pre>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">.IP</span>

</pre>

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">With A:min<avg\-cor_avg<max standing for : value of the position having minimal coverage in readsA.fasta < average coverage in readsA.fasta \- R\-squarred corrected average in readsA.fa < value of the position having maximal coverage in readsA.fasta</span>

</pre>

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">The coverage is the number of reads that perfectly mapped a position</span>

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">Any other situation (s not coherent with any): couple non read coherent, not outputed</span>

</pre>

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">.SH OPTIONS</span>

</pre>

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">.HP</span>

</pre>

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">\fB\-k\fR size_seed: will use seeds of length size_seed. Default: 25.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">.HP</span>

</pre>

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">\fB\-O\fR minimal_read_overlap: a read can be mapped if its overlap is a least "minimal_read_overlap". Default: k</span>

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">.HP</span>

</pre>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">\fB\-c\fR min_coverage: a sequence is covered by at least min_coverage coherent reads. Default: 2</span>

</pre>

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">.HP</span>

</pre>

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">\fB\-d\fR max_substitutions: Maximal number of substitutions authorized between a read and a fragment. Note that no substitution is allowed on the central position while anaylizing the kissnp output. Default: 1.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">.HP</span>

</pre>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">\fB\-o\fR file_name: write read\-coherent outputs. Default: standard output</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">.HP</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

33

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">\fB\-u\fR file_name: write unread\-coherent outputs. Default: standard output</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">.HP</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">\fB\-n\fR the input file (toCheck.fasta) is a kissnp output (incompatible with \fB\-I\fR option)</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

36

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">.IP</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

37

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">in this case: 1/ only the upper characters are considered (no mapping done on the extensions) and 2/ the central position (where the SNP occurs) is strictly mapped, no subsitution is authorized on this position.</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

38

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">.HP</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">\fB\-I\fR the input file (toCheck.fasta) is an Intl output (incompatible with \fB\-n\fR option)</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">.HP</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">\fB\-i\fR index_stride (int value). This is a heuristic for limiting the memory footprint. Instead of indexing each kmer of the sequences contained into the toCheck.fasta, kissreads indexes kmers occurring each "index_stride" position. Default = 1 (no heuristic)</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

42

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">.HP</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">\fB\-t\fR max number of threads (also limited by number of input files)</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

44

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">.HP</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">\fB\-m\fR align_file, write a file of reads mapped to sequences in file align_file</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

46

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">.HP</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

47

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">\fB\-s\fR silent mode</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

48

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">.HP</span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">\fB\-f\fR outputs coherent events in a standard fasta file format</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

50

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">.HP</span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

51

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">\fB\-h\fR prints this message and exit</span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">.SH AUTHOR</span>

</pre>

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.</span></pre>

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<br>

</li>

<li id="6935db46e89a5d49d7a15ca8202a1f2fae9c3ffd">

<a href="https://salsa.debian.org/med-team/mapsembler2/compare/dd6a079ef642cf7cd2a0c4c9f215794aa6553401...3f6a046f42cfd67ed124b31341454defacd9d138#6935db46e89a5d49d7a15ca8202a1f2fae9c3ffd"><strong>debian/mans/mapsembler2_kissreads_graph.1</strong></a>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.7.</span>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH MAPSEMBLER2_KISSREADS_GRAPH "1" "October 2018" "mapsembler2_kissreads_graph 2.2.4" "User Commands"</span>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.SH NAME</span>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">mapsembler2_kissreads_graph \- maps the provided reads on the graph</span>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.B mapsembler2_kissreads_graph</span>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">input_graph <readsC1.fasta/fastq[.gz]> [<readsC2.fasta/fastq[.gz]> [<readsC3.fasta/fastq[.gz] ...] \fB\-M\fR \fB\-t\fR type [\-k value] [\-c min_coverage] [\-d max_substitutions] [\-o name] [\-h]</span>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.SH DESCRIPTION</span>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">mapsembler2_kissreads_graph maps the provided reads on the graph</span>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">With option "\-t coverage": outputs an equivalent graph removing uncovered edges and adding:</span>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">.IP</span>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">for each node: the coverage per sample and per position</span>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">.IP</span>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">for each edge: the number of mapped reads per sample using this edge</span>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.P</span>

</pre>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">With option "-t modify": outputs the same simplified graph:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">.IP</span>

</pre>

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">removing low covered edges and nodes (less that min_coverage)</span>

</pre>

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">then phasing simple non branching paths</span>

</pre>

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20

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">.PP</span>

</pre>

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21

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">If \fB\-M\fR option is specified, the input is considered as a Mapsembler output \- thus composed of multiple independent graphes</span>

</pre>

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22

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">.SH OPTIONS</span>

</pre>

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23

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">.SS MANDATORY</span>

</pre>

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24

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">.HP</span>

</pre>

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25

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">\fB\-t\fR <type></span>

</pre>

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26

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">.IP</span>

</pre>

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27

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">"c" "coverage"</span>

</pre>

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28

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">.IP</span>

</pre>

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29

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">"m" "modify"</span>

</pre>

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">.SS OPTIONAL</span>

</pre>

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31

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">\fB\-M\fR: the input is considered as a Mapsembler output</span>

</pre>

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32

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">.HP</span>

</pre>

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">\fB\-o\fR file_name: write obtained graph. Default: standard output</span>

</pre>

</td>

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">.HP</span>

</pre>

</td>

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">\fB\-k\fR size_seed: will use seeds of length size_seed. Default: 25.</span>

</pre>

</td>

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36

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">.HP</span>

</pre>

</td>

</tr>

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">\fB\-c\fR min_coverage: Will consider an edge as coherent if coverage (number of reads from all sets using this edge) is at least min_coverage. Default: 2</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

38

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">.HP</span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">\fB\-d\fR max_substitutions: Will map a read on the graph with at most max_substitutions substitutions. Default: 1</span>

</pre>

</td>

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<td class="diff-line-num new new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

40

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">.SH AUTHOR</span>

</pre>

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.</span></pre>

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</li>

<li id="997e9ed24cbaf48602d1a5783f534367b993f182">

<a href="https://salsa.debian.org/med-team/mapsembler2/compare/dd6a079ef642cf7cd2a0c4c9f215794aa6553401...3f6a046f42cfd67ed124b31341454defacd9d138#997e9ed24cbaf48602d1a5783f534367b993f182"><strong>debian/mans/mapsembler_extend.1</strong></a>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.7.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH MAPSEMBLER_EXTEND "1" "October 2018" "mapsembler_extend 2.2.4" "User Commands"</span>

</pre>

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3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.SH NAME</span>

</pre>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">mapsembler_extend \- extends a DNA sequence of interest given a set of reads, by computing a targeted micro assembly</span>

</pre>

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5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.B mapsembler_extend</span>

</pre>

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7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"><extrem_kmers.fasta> <readsC1.fasta> [<readsC2.fasta> [<readsC3.fasta] ...] [\-t extension_type] [\-k value] [\-c value] [\-g value] [\-i index_name] [\-o name] [\-h]</span>

</pre>

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8

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.SH DESCRIPTION</span>

</pre>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Mapsembler 2 extends a DNA sequence of interest given a set of reads, by computing a targeted micro assembly.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">.SH OPTIONS</span>

</pre>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">.HP</span>

</pre>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">\fB\-t\fR extension_type. Default: 1</span>

</pre>

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13

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">.IP</span>

</pre>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">1: a strict sequence: any branching stops the extension</span>

</pre>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.IP</span>

</pre>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">2: a consensus sequence: contiging approach</span>

</pre>

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17

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">.IP</span>

</pre>

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">3: a strict graph: any branching is conserved in the graph</span>

</pre>

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19

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">.IP</span>

</pre>

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">4: a consensus graph: "small" polymorphism is merged, but "large" structures are represented</span>

</pre>

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">.HP</span>

</pre>

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">\fB\-k\fR size_kmers: Size of the k\-mers used duriung the extension phase Default: 31. Accepted range, depends on the compilation (make k=42 for instance)</span>

</pre>

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">.HP</span>

</pre>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">\fB\-c\fR min_coverage: a sequence is covered by at least min_coverage coherent reads. Default: 2</span>

</pre>

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">.HP</span>

</pre>

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">\fB\-g\fR estimated_genome_size: estimation of the size of the genome whose reads come from.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">.IP</span>

</pre>

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">It is in bp, does not need to be accurate, only controls memory usage. Default: 3 billion</span>

</pre>

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">.HP</span>

</pre>

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">\fB\-x\fR node_len: limit max of nodes length. Default: 40</span>

</pre>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">.HP</span>

</pre>

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">\fB\-y\fR graph_max_depth: limit max of graph depth.Default: 10000</span>

</pre>

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">.HP</span>

</pre>

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">\fB\-i\fR index_name: stores the index files in files starting with this prefix name. Can be re\-used latter. Default: "index"</span>

</pre>

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">.IP</span>

</pre>

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">IF THE FILE "index_name.bloom" EXISTS: the index is not re\-created</span>

</pre>

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">.HP</span>

</pre>

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">\fB\-o\fR file_name_prefix: where to write outputs. Default: "res_mapsembler"</span>

</pre>

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">.HP</span>

</pre>

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">\fB\-p\fR search_mod: kind of prosses Breadth or Depth. Default: Breadth</span>

</pre>

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41

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">.HP</span>

</pre>

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42

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">\fB\-h\fR prints this message and exit</span>

</pre>

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43

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">.SH AUTHOR</span>

</pre>

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.</span></pre>

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<br>

</li>

<li id="105896cab3a29d651da9f1df968e932631fd91ee">

<a href="https://salsa.debian.org/med-team/mapsembler2/compare/dd6a079ef642cf7cd2a0c4c9f215794aa6553401...3f6a046f42cfd67ed124b31341454defacd9d138#105896cab3a29d651da9f1df968e932631fd91ee"><strong>debian/mans/run_mapsembler2_pipeline.1</strong></a>

<hr>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.7.</span>

</pre>

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2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH RUN_MAPSEMBLER2_PIPELINE "1" "October 2018" "run_mapsembler2_pipeline 2.2.4" "User Commands"</span>

</pre>

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3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.SH NAME</span>

</pre>

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4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">run_mapsembler2_pipeline \- pipelines the mapsembler2 tools</span>

</pre>

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5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>

</pre>

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6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.B run_mapsembler_and_phaser.sh</span>

</pre>

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7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">\fI\,-s <starter.fasta> -r <reads.faste> -t \/\fR[\fI\,1/2/3/4\/\fR]\fI\,<options>\/\fR</span>

</pre>

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8

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.SH DESCRIPTION</span>

</pre>

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9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">run_mapsembler_pipeline.sh, a pipelining mapsembler2_extremities, mapsembler2_extend and kissread_g</span>

</pre>

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10

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">.SH OPTIONS</span>

</pre>

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11

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">.HP</span>

</pre>

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12

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">\fB\-s\fR: file containing starters (fasta)</span>

</pre>

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13

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">.HP</span>

</pre>

</td>

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14

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">\fB\-r\fR list of reads separated by space, surrounded by the '"' character. Note that reads may be in fasta or fastq format, gzipped or not. Example: \fB\-r\fR "data_sample/reads_sequence1.fasta   data_sample/reads_sequence2.fasta.gz".</span>

</pre>

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15

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.HP</span>

</pre>

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16

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">\fB\-t\fR: kind of assembly: 1=unitig (fasta), 2=contig (fasta), 3=unitig (graph), 4=contig(graph)</span>

</pre>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">.SS OPTIONAL</span>

</pre>

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">.HP</span>

</pre>

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">\fB\-p\fR prefix. All out files will start with this prefix. Example: \fB\-p\fR my_prefix</span>

</pre>

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">.HP</span>

</pre>

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">\fB\-k\fR value. Set the length of used kmers. Must fit the compiled value. Default=31. Example \fB\-k\fR 31</span>

</pre>

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">.HP</span>

</pre>

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">\fB\-c\fR value. Set the minimal coverage. Default=5. Example \fB\-c\fR 5</span>

</pre>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">.HP</span>

</pre>

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">\fB\-d\fR value. Set the number of authorized substitutions used while mapping reads on found SNPs. Default=1. Example: \fB\-d\fR 1</span>

</pre>

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">.HP</span>

</pre>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">\fB\-g\fR value. Estimated genome size. Used only to control memory usage. e.g. 3 billion (3000000000) uses 4Gb of RAM. Default=10 million. Example: \fB\-d\fR 10000000</span>

</pre>

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">.HP</span>

</pre>

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">\fB\-f\fR value. Set the process of search in the graph (1=Breadth  and 2=Depth). Default=1. Example: \fB\-f\fR 1</span>

</pre>

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">.HP</span>

</pre>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">\fB\-x\fR value. Set the maximal nodes length . Default=40. Example: \fB\-x\fR 40</span>

</pre>

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">.HP</span>

</pre>

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">\fB\-y\fR value. Set the maximal graph depth . Default=10000. Example: \fB\-y\fR 10000</span>

</pre>

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">.HP</span>

</pre>

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">\fB\-h\fR Prints this message and exist</span>

</pre>

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">.SH SEE ALSO</span>

</pre>

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">Any further question: read the readme file or contact us: pierre.peterlongo@inria.fr</span>

</pre>

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">.SH AUTHOR</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.</span></pre>

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<br>

</li>

<li id="2599798e0a9deb7e9830d61d9024c3d8c0aee3be">

<a href="https://salsa.debian.org/med-team/mapsembler2/compare/dd6a079ef642cf7cd2a0c4c9f215794aa6553401...3f6a046f42cfd67ed124b31341454defacd9d138#2599798e0a9deb7e9830d61d9024c3d8c0aee3be"><strong>debian/mapsembler2.manpages</strong></a>

<hr>

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">mapsembler2_extremities.1</span>

</pre>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">mapsembler_extend.1</span>

</pre>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">mapsembler2_kissreads.1</span>

</pre>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">mapsembler2_kissreads_graph.1</span>

</pre>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">run_mapsembler2_pipeline.1</span>

</pre>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"></span></pre>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/mans/*.1</span></pre>

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<br>

</li>

<li id="4bf5c375f6de83c6b39cea4b73262a3f9f1e0002">

<a href="https://salsa.debian.org/med-team/mapsembler2/compare/dd6a079ef642cf7cd2a0c4c9f215794aa6553401...3f6a046f42cfd67ed124b31341454defacd9d138#4bf5c375f6de83c6b39cea4b73262a3f9f1e0002"><strong>debian/patches/fix_build</strong>

deleted

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff">Subject: Add hardening</span>

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2

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff">Description: makefiles do not import default CFLAGS,...</span>

</pre>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff">this patch add debian cflags for hardening</span>

</pre>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff">Forwarded: no</span>

</pre>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff">Author: Olivier Sallou <osallou@debian.org></span>

</pre>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff">Last-Updated: 2014-02-01</span>

</pre>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/minia/makefile</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/minia/makefile</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,5 +1,9 @@</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> CC=g++</span>

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-CFLAGS = -O4</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS)</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

14

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CFLAGS = $(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS) -O4</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

15

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

16

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

17

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> SRC=Pool.cpp Bank.cpp Bloom.cpp Hash16.cpp LargeInt.cpp Kmer.cpp Terminator.cpp Traversal.cpp LinearCounter.cpp Set.cpp Utils.cpp SortingCount.cpp Debloom.cpp OAHash.cpp</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

18

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"> EXEC=minia</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

19

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"> OBJ= $(SRC:.cpp=.o)</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -60,7 +64,7 @@</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

21

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"> all: $(EXEC)</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"> </span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"> minia: clean $(OBJ) Minia.cpp</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

24

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(CC) -o $@ $(OBJ) Minia.cpp $(CFLAGS) -lz</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

25

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CC) -o $@ $(OBJ) Minia.cpp $(CFLAGS) $(LDFLAGS) -lz</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

26

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"> </span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

27

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"> %.o: %.cpp %.h</span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

28

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff">  $(CC) -o $@ -c $< $(CFLAGS)</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/maps/makefile</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

30

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/maps/makefile</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

31

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,7 +1,10 @@</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"> CC=g++ </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"> EXEC=mapsembler</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"> #CFLAGS=  -O4 -lz --std=gnu++0x</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-CFLAGS=  -g -lz -DMINIA_IS_IN_PARENT_FOLDER</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS)</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CFLAGS = $(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS) -g -lz -DMINIA_IS_IN_PARENT_FOLDER</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS)</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

39

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

40

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC40" class="line" lang="diff"> #CFLAGS=  -O3 -lz -DMINIA_IS_IN_PARENT_FOLDER</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

41

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC41" class="line" lang="diff"> #CFLAGS=  -g -lz --std=gnu++0x -DMINIA_IS_IN_PARENT_FOLDER</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC42" class="line" lang="diff"> #CFLAGS=  -g -lz -DMINIA_IS_IN_PARENT_FOLDER</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC43" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -49,7 +52,7 @@</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC44" class="line" lang="diff"> </span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

45

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC45" class="line" lang="diff"> mapsembler:  $(OBJ) $(OBJ2) mapsembler.cpp</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC46" class="line" lang="diff"> #mapsembler:  $(OBJ) $(OBJ2) test.cpp</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

47

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC47" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(CC) -o $@ $^ $(CFLAGS) </span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

48

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC48" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CC) -o $@ $^ $(CFLAGS) $(LDFLAGS)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

49

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC49" class="line" lang="diff"> </span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

50

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC50" class="line" lang="diff"> %.o: %.cpp %.h </span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

51

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC51" class="line" lang="diff">  $(CC) -lz -o $@ -c $< $(CFLAGS)</span>

</pre>

</td>

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<pre style="margin: 0;">-<span id="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/kissreads_g/makefile</span></span>

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<pre style="margin: 0;">-<span id="LC53" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/kissreads_g/makefile</span></span>

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<pre style="margin: 0;">-<span id="LC54" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -4,7 +4,9 @@</span></span>

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<pre style="margin: 0;">-<span id="LC55" class="line" lang="diff"> #Loader.cpp CFLAGS=  -g -lz -std=c++11 -DMINIA_IS_IN_PARENT_FOLDER</span>

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<pre style="margin: 0;">-<span id="LC56" class="line" lang="diff"> #Loader.cpp </span>

</pre>

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<pre style="margin: 0;">-<span id="LC57" class="line" lang="diff"> #CFLAGS=  -O3 -lz -DMINIA_IS_IN_PARENT_FOLDER</span>

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<pre style="margin: 0;">-<span id="LC58" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-CFLAGS=  -g -lz -DMINIA_IS_IN_PARENT_FOLDER</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC59" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC60" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CFLAGS = $(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS) -g -lz -DMINIA_IS_IN_PARENT_FOLDER</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC61" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC62" class="line" lang="diff"> SRC=block_allocator.cpp  DeBruijnGraph.cpp  Fragment.cpp  json.cpp  read_coherence_mapsembler/libchash.cpp     read_coherence_mapsembler/couple.cpp  read_coherence_mapsembler/misc_tools.cpp  read_coherence_mapsembler/read_groups.cpp read_coherence_mapsembler/consensus_common.cpp  read_coherence_mapsembler/list.cpp    read_coherence_mapsembler/read_coherence.cpp  read_coherence_mapsembler/interface_libchash.cpp commons.cpp ../minia/Kmer.cpp ../minia/Bank.cpp Loader.cpp BooleanVector.cpp ReadMapper.cpp</span>

</pre>

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<pre style="margin: 0;">-<span id="LC63" class="line" lang="diff"> OBJ= $(SRC:.cpp=.o) </span>

</pre>

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<pre style="margin: 0;">-<span id="LC64" class="line" lang="diff"> all: $(EXEC)</span>

</pre>

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<pre style="margin: 0;">-<span id="LC65" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -48,7 +50,7 @@</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC66" class="line" lang="diff"> all: $(EXEC)</span>

</pre>

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<pre style="margin: 0;">-<span id="LC67" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC68" class="line" lang="diff"> kissreads_graph:  $(OBJ) KissReadsGraph.cpp</span>

</pre>

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<pre style="margin: 0;">-<span id="LC69" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(CC) -o $@ $^ $(CFLAGS)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC70" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CC) -o $@ $^ $(CFLAGS) $(LDFLAGS)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC71" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC72" class="line" lang="diff"> %.o: %.cpp %.h</span>

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<pre style="margin: 0;">-<span id="LC73" class="line" lang="diff">  $(CC) -lz -o $@ -c $< $(CFLAGS)</span></pre>

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<br>

</li>

<li id="b82cc53a96d198b42d2cf5ccdce4b085dbfb94ca">

<a href="https://salsa.debian.org/med-team/mapsembler2/compare/dd6a079ef642cf7cd2a0c4c9f215794aa6553401...3f6a046f42cfd67ed124b31341454defacd9d138#b82cc53a96d198b42d2cf5ccdce4b085dbfb94ca"><strong>debian/patches/fix_makefile</strong>

deleted

</a>

<hr>

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff">Subject: Add hardening</span>

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2

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff">Description: makefiles do not import default CFLAGS,...</span>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff">this patch add debian cflags for hardening</span>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff">Forwarded: no</span>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff">Author: Olivier Sallou <osallou@debian.org></span>

</pre>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff">Last-Updated: 2014-02-21</span>

</pre>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/maps/makefile</span></span>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/maps/makefile</span></span>

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -49,11 +49,16 @@</span></span>

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"> mapsembler:  $(OBJ) $(OBJ2) mapsembler.cpp</span>

</pre>

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"> #mapsembler:  $(OBJ) $(OBJ2) test.cpp</span>

</pre>

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(CC) -o $@ $^ $(CFLAGS) </span></span>

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CC) -o $@ $^ $(CFLAGS) $(LDFLAGS)</span></span>

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"> %.o: %.cpp %.h </span>

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff">  $(CC) -lz -o $@ -c $< $(CFLAGS)</span>

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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CPPFLAGS=$(shell dpkg-buildflags --get CPPFLAGS)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CFLAGS += $(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS)</span></span>

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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+LDFLAGS=$(shell dpkg-buildflags --get LDFLAGS)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"> #%.o: %.c %.h </span>

</pre>

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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"> #        $(CC) -o $@ -c $< $(CFLAGS)</span></pre>

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<br>

</li>

<li id="94fea411c7d9c972414b101a25bd83389ecffb01">

<a href="https://salsa.debian.org/med-team/mapsembler2/compare/dd6a079ef642cf7cd2a0c4c9f215794aa6553401...3f6a046f42cfd67ed124b31341454defacd9d138#94fea411c7d9c972414b101a25bd83389ecffb01"><strong>debian/patches/fix_path</strong>

deleted

</a>

<hr>

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1

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff">Subject: use Debian paths</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff">Description: update some paths to use Debian package paths</span>

</pre>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff">Last-Updated: 2014-02-01</span>

</pre>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff">Author: Olivier Sallou <osallou@debian.org></span>

</pre>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff">Forwarded: no</span>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/run_mapsembler_and_phaser.sh</span></span>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/run_mapsembler_and_phaser.sh</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,8 +1,9 @@</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/bin/bash</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> #######################################################################</span>

</pre>

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"> #################### HEADER, CHANGE VALUES HERE #######################</span>

</pre>

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"> #######################################################################</span>

</pre>

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-starters_file="sample_example/fragments.fa"</span></span>

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-read_sets="sample_example/reads.fa" # FOR instance: "read_set1.fa.gz read_set2.fq.gz"</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+starters_file="/usr/share/doc/mapsembler2/sample_example/fragments.fa"</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+read_sets="/usr/share/doc/mapsembler2/sample_example/reads.fa.gz" # FOR instance: "read_set1.fa.gz read_set2.fq.gz"</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> prefix_index="index" # all files used for indexing will be written will start with this prefix</span>

</pre>

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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"> prefix_results="res" # all final files will be written will start with this prefix</span>

</pre>

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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"> k=31 # size of kmers</span>

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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -10,7 +11,7 @@</span></span>

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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"> d=1 # estimated number of error per read (used by kissreads only)</span>

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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"> g=10000000 # estimated genome size. Used only to control kissnp2 memory usage. e.g. 3 billion (3000000000) uses 4Gb of RAM.</span>

</pre>

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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"> t=0</span>

</pre>

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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-PATH_TOOLS="./tools/" # path were executables kissnp2 and kissreads are. Leave blank if they are located in a directory located in the PATH environnement variable</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+PATH_TOOLS="/usr/bin/" # path were executables kissnp2 and kissreads are. Leave blank if they are located in a directory located in the PATH environnement variable</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"> #######################################################################</span>

</pre>

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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"> #################### END HEADER                 #######################</span>

</pre>

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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"> #######################################################################</span></pre>

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<br>

</li>

<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

<a href="https://salsa.debian.org/med-team/mapsembler2/compare/dd6a079ef642cf7cd2a0c4c9f215794aa6553401...3f6a046f42cfd67ed124b31341454defacd9d138#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,3 +4,4 @@ add_hardening</td>

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4

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">skip_mphe</span>

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5

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">gcc-5.patch</span>

</pre>

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6

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">libgomp.patch</span>

</pre>

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7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">spelling.patch</span></pre>

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<br>

</li>

<li id="45ae034d1d71b2d961abb7c91cf3d2f1a02a59c6">

<a href="https://salsa.debian.org/med-team/mapsembler2/compare/dd6a079ef642cf7cd2a0c4c9f215794aa6553401...3f6a046f42cfd67ed124b31341454defacd9d138#45ae034d1d71b2d961abb7c91cf3d2f1a02a59c6"><strong>debian/patches/spelling.patch</strong></a>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Description: Fix spelling</span>

</pre>

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2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>

</pre>

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3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Last-Update: Wed, 10 Oct 2018 12:49:34 +0200</span>

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4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>

</pre>

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5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/kissreads_graph/KissReadsGraph.cpp</span></span>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/kissreads_graph/KissReadsGraph.cpp</span></span>

</pre>

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7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -35,7 +35,7 @@ void print_usage_and_exit(char * name){</span></span>

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8

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff">   fprintf (stderr, "With option \"-t modify\": outputs the same simplified graph:\n");</span>

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9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff">   fprintf (stderr, "\t removing low covered edges and nodes (less that min_coverage)\n");</span>

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10

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff">     fprintf (stderr, "\t then phasing simple non branching paths\n");</span>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    fprintf (stderr, "If -M option is specified, the input is considered as a Mapsembler output - thus composed of multiple independant graphes\n");</span></span>

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12

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    fprintf (stderr, "If -M option is specified, the input is considered as a Mapsembler output - thus composed of multiple independent graphes\n");</span></span>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff">     </span>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff">     </span>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff">  fprintf (stderr, "\nMANDATORY\n");</span>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/mapsembler2_extend/IterativeExtensions.cpp</span></span>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/mapsembler2_extend/IterativeExtensions.cpp</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -178,7 +178,7 @@ void IterativeExtensions::construct_line</span></span>

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff">             revcomp_sequence(kmer_seq,sizeKmer);</span>

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20

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

21

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff">         if (debug)</span>

</pre>

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22

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            printf(" --- iteration: kmer %s%s (of lenght %d) depth %d nbNodes explored %lli ---\n",kmer_seq,strand?" (internally rc)":"", (int)strlen(kmer_seq), depth,nbNodes);</span></span>

</pre>

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23

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            printf(" --- iteration: kmer %s%s (of length %d) depth %d nbNodes explored %lli ---\n",kmer_seq,strand?" (internally rc)":"", (int)strlen(kmer_seq), depth,nbNodes);</span></span>

</pre>

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24

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> </span>

</pre>

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25

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff">         // right extension</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

26

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff">         int len_right = traversal->traverse(kmer,right_traversal,strand);</span>

</pre>

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27

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -397,7 +397,7 @@ void IterativeExtensions::construct_line</span></span>

</pre>

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28

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff">             revcomp_sequence(kmer_seq,sizeKmer);</span>

</pre>

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29

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff">         </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

30

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff">         if (debug)</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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31

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            printf("iteration: kmer %s%s (of lenght %zu) depth %d nbNodes explored %lli\n",kmer_seq,strand?" (internally rc)":"", strlen(kmer_seq), depth,nbNodes);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

32

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            printf("iteration: kmer %s%s (of length %zu) depth %d nbNodes explored %lli\n",kmer_seq,strand?" (internally rc)":"", strlen(kmer_seq), depth,nbNodes);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

33

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff">         </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

34

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff">         // right extension</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

35

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff">         int len_right = traversal->traverse(kmer,right_traversal,strand);</span></pre>

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<br>

</li>

<li id="8756c63497c8dc39f7773438edf53b220c773f67">

<a href="https://salsa.debian.org/med-team/mapsembler2/compare/dd6a079ef642cf7cd2a0c4c9f215794aa6553401...3f6a046f42cfd67ed124b31341454defacd9d138#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7,7 +7,7 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all</td>

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7

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7

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>

</pre>

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8

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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">DEB_HOST_MULTIARCH ?= $(shell dpkg-architecture -qDEB_HOST_MULTIARCH)</span>

</pre>

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9

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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

9

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"><span class="idiff left right">SRC_VERSION =$(shell dpkg-parsechangelog | sed -ne 's/^Version: \(\([0-9]\+\):\)\?\(.*\)-.*/\3/p')</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"><span class="idiff left right">include /usr/share/dpkg/default.mk</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">ifneq ($(wildcard /usr/include/hdf5/serial),)</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">  export DEB_CPPFLAGS_MAINT_APPEND := -I/usr/include/hdf5/serial</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -22,9 +22,6 @@ LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS)</td>

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<td class="diff-line-num old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">%:</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">     dh $@</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext">get-orig-source:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext">     uscan --verbose --force-download</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">override_dh_auto_build:</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">     mkdir mapsembler2_extremities/build</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">     cd mapsembler2_extremities/build && cmake .. && make</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -42,20 +39,10 @@ override_dh_clean:</td>

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<td class="diff-line-num old_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

39

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext">     cd kissreads && make clean</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext">     rm -f kissreads/mapsembler2_kissreads</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

41

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC45" class="line" lang="plaintext">     rm -f mapsembler2_extremities.1</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC46" class="line" lang="plaintext">     rm -f mapsembler_extend.1</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

47

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<td class="diff-line-num new_line old" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC47" class="line" lang="plaintext">     rm -f kissreads.1</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

48

</td>

<td class="diff-line-num new_line old" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC48" class="line" lang="plaintext">     rm -f kissreads_graph.1</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

49

</td>

<td class="diff-line-num new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

42

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext">     dh_clean</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

50

</td>

<td class="diff-line-num new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

43

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

51

</td>

<td class="diff-line-num new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

44

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext">override_dh_install:</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

52

</td>

<td class="diff-line-num new_line old" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC52" class="line" lang="plaintext">     help2man --help-option=-h --no-discard-stderr --version-string=$(SRC_VERSION) ./mapsembler2_extremities/build/mapsembler2_extremities > mapsembler2_extremities.1</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

53

</td>

<td class="diff-line-num new_line old" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC53" class="line" lang="plaintext">     help2man --help-option=-h --no-discard-stderr --version-string=$(SRC_VERSION) ./mapsembler2_extend/mapsembler_extend > mapsembler_extend.1</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

54

</td>

<td class="diff-line-num new_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

45

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext">     mv ./kissreads/kissreads ./kissreads/mapsembler2_kissreads</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

55

</td>

<td class="diff-line-num new_line old" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC55" class="line" lang="plaintext">     help2man --help-option=-h --no-discard-stderr --version-string=$(SRC_VERSION) ./kissreads/mapsembler2_kissreads > mapsembler2_kissreads.1</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

56

</td>

<td class="diff-line-num new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

46

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext">     mv ./kissreads_graph/kissreads_graph ./kissreads_graph/mapsembler2_kissreads_graph</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

57

</td>

<td class="diff-line-num new_line old" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC57" class="line" lang="plaintext">     help2man --help-option=-h --no-discard-stderr --version-string=$(SRC_VERSION) ./kissreads_graph/mapsembler2_kissreads_graph > mapsembler2_kissreads_graph.1</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

58

</td>

<td class="diff-line-num new_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

47

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext">     cp run_mapsembler2_pipeline.sh run_mapsembler2_pipeline</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

59

</td>

<td class="diff-line-num new_line old" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC59" class="line" lang="plaintext">     help2man --help-option=-h --no-discard-stderr --version-string=$(SRC_VERSION) ./run_mapsembler2_pipeline > run_mapsembler2_pipeline.1</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

60

</td>

<td class="diff-line-num new_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

48

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext">     dh_install</span></pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

61

</td>

<td class="diff-line-num new_line old" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC61" class="line" lang="plaintext"></span></pre>

</td>

</tr>

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